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| Item Type: | Article |
|---|---|
| Title: | G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-hairpin-duplex switch |
| Creators Name: | Kaplan, O.I., Berber, B., Hekim, N. and Doluca, O. |
| Abstract: | Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns. |
| Keywords: | Bacterial DNA, Bacterial Genome, Consensus Sequence, Escherichia coli, G-Quadruplexes, Gene Ontology, Inverted Repeat Sequences, Nucleic Acid Conformation, Nucleotide Motifs, Phylogeny, Position-Specific Scoring Matrices |
| Source: | Nucleic Acids Research |
| ISSN: | 0305-1048 |
| Publisher: | Oxford University Press |
| Volume: | 44 |
| Number: | 19 |
| Page Range: | 9083-9095 |
| Date: | 2 November 2016 |
| Official Publication: | https://doi.org/10.1093/nar/gkw769 |
| PubMed: | View item in PubMed |
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